dragen-results-utils 0.1.0

Collection of Python scripts for post-processing Illumina DRAGEN results output files.

Collection of Python scripts for post-processing Illumina DRAGEN results output files.

Exported Console scripts

• analyze-dragen-results

analyze-dragen-results --vcf_file examples/sample_001.vcf --metrics_file examples/sample_001.variant_metrics.csv
--outdir was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758'
Created output directory '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758'
--logfile was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log'
--figure_file was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.quality_distribution.png'
--variant_summary_report_file was not specified and therefore was set to
'/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.variant_summary_report.txt'
--metrics_summary_report_file was not specified and therefore was set to
'/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.metrics_summary_report.txt'

Contents of the variant summary report file:

cat /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.variant_summary_report.txt
## method-created: /tmp/test-dragen-results-utils/venv/lib/python3.10/site-packages/dragen_results_utils/analyzer.py
## date-created: 2025-02-27-171759
## created-by: sundaram
## vcf-file: /tmp/examples/sample_001.vcf
## metrics-file: /tmp/examples/sample_001.variant_metrics.csv
## logfile: /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log
Total_Variants: 5
Passed_Filters: 4
Average_QUAL: 39.44

Contents of the metrics summary report file:

cat /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.metrics_summary_report.txt
## method-created: /tmp/test-dragen-results-utils/venv/lib/python3.10/site-packages/dragen_results_utils/analyzer.py
## date-created: 2025-02-27-171759
## created-by: sundaram
## vcf-file: /tmp/examples/sample_001.vcf
## metrics-file: /tmp/examples/sample_001.variant_metrics.csv
## logfile: /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log
METRIC: VALUE
Total SNPs: 4.0
Total Indels: 1.0
Ti/Tv Ratio: 2.0
Heterozygosity Rate: 0.6
Variants Passing Filters: 4.0
Mean Variant Quality: 39.44